SMTL ID : 3wqd.1

D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with D-erythro-3-hydroxyaspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: H.51, K.53, A.94, R.151, H.182, Y.187, G.226, S.227, T.228, P.229, R.244, A.245, G.246, V.247 Ligands: 999.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.94, A:H.182 Hydrogen bonds: A:R.151, A:R.151, A:Y.187, A:T.228, A:R.244, A:G.246, A:V.247 Water bridges: A:H.51, A:K.53, A:K.53, A:K.53, A:A.94 Salt bridges: A:K.53, A:H.182 pi-Stacking: A:H.51, A:H.182 PLP.5: 15 residues within 4Å: Chain B: H.51, K.53, A.94, R.151, H.182, Y.187, G.226, S.227, T.228, P.229, R.244, A.245, G.246, V.247 Ligands: 999.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:A.94, B:H.182 Hydrogen bonds: B:R.151, B:R.151, B:T.228, B:T.228, B:R.244, B:G.246, B:V.247 Water bridges: B:K.53, B:Y.187, B:Y.187 Salt bridges: B:K.53, B:H.182 pi-Stacking: B:H.51, B:H.182

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Y.187, H.361, C.363 Ligands: 999.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.361, A:C.363, H2O.4, H2O.5, H2O.16 MG.4: 3 residues within 4Å: Chain A: H.150 Chain B: N.328 Ligands: 999.3 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: K.53, Y.187, H.361, C.363 Ligands: 999.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.361, B:C.363, H2O.3, H2O.17, H2O.18 MG.7: 3 residues within 4Å: Chain A: N.328 Chain B: H.150 Ligands: 999.8 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: W.390 No protein-ligand interaction detected (PLIP)

2 x 999: (3S)-3-hydroxy-D-aspartic acid(Non-covalent)

999.3: 11 residues within 4Å: Chain A: K.53, H.150, R.151, H.182, Y.187, H.361 Chain B: N.328, Q.329 Ligands: PLP.1, MG.2, MG.4 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.53, A:R.151, B:Q.329 Water bridges: A:H.150, A:H.150, A:R.151, A:R.151, B:N.328, B:N.328, B:N.328, B:H.331 Salt bridges: A:K.53, A:R.151, A:H.361 999.8: 11 residues within 4Å: Chain A: N.328, Q.329 Chain B: K.53, H.150, R.151, H.182, Y.187, H.361 Ligands: PLP.5, MG.6, MG.7 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:Q.329, B:K.53, B:R.151, B:Y.187 Water bridges: A:R.295, A:N.328, A:N.328, A:N.328, A:H.331, B:K.53, B:H.150, B:H.150, B:R.151, B:R.151 Salt bridges: B:K.53, B:K.53, B:R.151, B:H.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, Y. et al., Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate. Appl.Microbiol.Biotechnol. (2015)

Release Date

2015-01-28

Peptides

D-threo-3-hydroxyaspartate dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-threo-3-hydroxyaspartate dehydratase

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